1VK6 | pdb_00001vk6

Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VK6/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-04-30 Released: 2004-05-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 31.98 kDa 
• Atom Count: 2,193 
• Modeled Residue Count: 257 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH pyrophosphatase	A	269	Escherichia coli K-12	Mutation(s): 8  Gene Names: NUDC, B3996 EC: 3.6.1 (PDB Primary Data), 3.6.1.22 (UniProt)
UniProt
Find proteins for P32664 (Escherichia coli (strain K12)) Explore P32664  Go to UniProtKB:  P32664

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A], E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VK6

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.319	α = 90
b = 127.319	β = 90
c = 108.405	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-05-11
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary